54 research outputs found

    Structural communication between the GTPase Sec4p and its activator Sec2p: Determinants of GEF activity and early deformations to nucleotide release

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    Ras GTPases are molecular switches that cycle between OFF and ON states depending on the bound nucleotide (i.e. GDP-bound and GTP-bound, respectively). The Rab GTPase, Sec4p, plays regulatory roles in multiple steps of intracellular vesicle trafficking. Nucleotide release is catalyzed by the Guanine Nucleotide Exchange Factor (GEF) Sec2p. Here, the integration of structural information with molecular dynamics (MD) simulations addressed a number of questions concerning the intrinsic and stimulated dynamics of Sec2p and Sec4p as well as the chain of structural deformations leading to GEF-assisted activation of the Rab GTPase. Sec2p holds an intrinsic ability to adopt the conformation found in the crystallographic complexes with Sec4p, thus suggesting that the latter selects and shifts the conformational equilibrium towards a pre-existing bound-like conformation of Sec2p. The anchoring of Sec4p to a suitable conformation of Sec2p favors the Sec2p-assisted pulling on itself of the α1/switch 1 (SWI) loop and of SWI, which loose any contact with GDP. Those deformations of Sec4p would occur earlier. Formation of the final Sec2p-Sec4p hydrophobic interface, accomplishes later. Disruption of the nucleotide cage would cause firstly loss of interactions with the guanine ring and secondly loss of interactions with the phosphates. The ease in sampling the energy landscape and adopting a bound-like conformation likely favors the catalyzing ability of GEFs for Ras GTPases

    Wordom update 2: A user-friendly program for the analysis of molecular structures and conformational ensembles

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    We present the second update of Wordom, a user-friendly and efficient program for manipulation and analysis of conformational ensembles from molecular simulations. The actual update expands some of the existing modules and adds 21 new modules to the update 1 published in 2011. The new adds can be divided into three sets that: 1) analyze atomic fluctuations and structural communication; 2) explore ion-channel conformational dynamics and ionic translocation; and 3) compute geometrical indices of structural deformation. Set 1 serves to compute correlations of motions, find geometrically stable domains, identify a dynamically invariant core, find changes in domain-domain separation and mutual orientation, perform wavelet analysis of large-scale simulations, process the output of principal component analysis of atomic fluctuations, perform functional mode analysis, infer regions of mechanical rigidity, analyze overall fluctuations, and perform the perturbation response scanning. Set 2 includes modules specific for ion channels, which serve to monitor the pore radius as well as water or ion fluxes, and measure functional collective motions like receptor twisting or tilting angles. Finally, set 3 includes tools to monitor structural deformations by computing angles, perimeter, area, volume, β-sheet curvature, radial distribution function, and center of mass. The ring perception module is also included, helpful to monitor supramolecular self-assemblies. This update places Wordom among the most suitable, complete, user-friendly, and efficient software for the analysis of biomolecular simulations. The source code of Wordom and the relative documentation are available under the GNU general public license at http://wordom.sf.net

    Network and atomistic simulations unveil the structural determinants of mutations linked to retinal diseases

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    A number of incurable retinal diseases causing vision impairments derive from alterations in visual phototransduction. Unraveling the structural determinants of even monogenic retinal diseases would require network-centered approaches combined with atomistic simulations. The transducin G38D mutant associated with the Nougaret Congenital Night Blindness (NCNB) was thoroughly investigated by both mathematical modeling of visual phototransduction and atomistic simulations on the major targets of the mutational effect. Mathematical modeling, in line with electrophysiological recordings, indicates reduction of phosphodiesterase 6 (PDE) recognition and activation as the main determinants of the pathological phenotype. Sub-microsecond molecular dynamics (MD) simulations coupled with Functional Mode Analysis improve the resolution of information, showing that such impairment is likely due to disruption of the PDEgamma binding cavity in transducin. Protein Structure Network analyses additionally suggest that the observed slight reduction of theRGS9-catalyzed GTPase activity of transducin depends on perturbed communication between RGS9 and GTP binding site. These findings provide insights into the structural fundamentals of abnormal functioning of visual phototransduction caused by a missense mutation in one component of the signaling network. This combination of network-centered modeling with atomistic simulations represents a paradigm for future studies aimed at thoroughly deciphering the structural determinants of genetic retinal diseases. Analogous approaches are suitable to unveil the mechanism of information transfer in any signaling network either in physiological or pathological conditions

    The response of the algae Fucus virsoides (Fucales, Ochrophyta) to Roundup® solution exposure: A metabolomics approach

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    8noGlyphosate, as a broad-spectrum herbicide, is frequently detected in water and several studies have investigated its effects on several freshwater aquatic organisms. Yet, only few investigations have been performed on marine macroalgae. Here, we studied both the metabolomics responses and the effect on primary production in the endemic brown algae Fucus virsoides exposed to different concentration (0, 0.5, 1.5 and 2.5 mg L−1) of a commercial glyphosate-based herbicide, namely Roundup®. Our results show that Roundup® significantly reduced quantum yield of photosynthesis (Fv/Fm) and caused alteration in the metabolomic profiles of exposed thalli compared to controls. Together with the decrease in the aromatic amino acids (phenylalanine and tyrosine), an increase in shikimate content was detected. The branched-amino acids differently varied according to levels of herbicide exposure, as well as observed for the content of choline, formate, glucose, malonate and fumarate. Our results suggest that marine primary producers could be largely affected by the agricultural land use, this asking for further studies addressing the ecosystem-level effects of glyphosate-based herbicides in coastal waters.partially_openopenFelline, Serena; Del Coco, Laura; Kaleb, Sara; Guarnieri, Giuseppe; Fraschetti, Simonetta; Terlizzi, Antonio; Fanizzi, Francesco Paolo; Falace, AnnalisaFelline, Serena; Del Coco, Laura; Kaleb, Sara; Guarnieri, Giuseppe; Fraschetti, Simonetta; Terlizzi, Antonio; Fanizzi, Francesco Paolo; Falace, Annalis

    Preliminary observations of caulerpin accumulation from the invasive Caulerpa cylindracea in native Mediterranean fish species

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    Recent studies have shown that the Mediterranean white sea bream Diplodus sargus includes the invasive green alga Caulerpa cylindracea in its diet, with consequent metabolic and enzymatic alterations. As a result of this novel alimentary habit, the bioactive algal red pigment caulerpin has been detected in its tissues. However, this may not be an isolated case: other fish species have also been reported to feed on C. cylindracea, although the possible accumulation of caulerpin in their tissues has not yet been investigated. In this report, we analysed stomach contents and caulerpin levels in the native sparid species Spondyliosoma cantharus, Sarpa salpa, and Diplodus vulgaris, and in the scarid Sparisoma cretense, along with the Lessepsian siganid Siganus luridus. C. cylindracea was found in the stomachs of all but one fish species, the exception being S. cretense, in which prey items could not be determined due to the high degree of digestion. Chemical analysis of fish tissues revealed that only S. cantharus and S. salpa accumulated caulerpin, while no traces of the compound were detected in the other species. Despite intense research efforts on natural products obtained from C. cylindracea, a complete picture of the impacts caused by fish including this alga in their diet has not been elucidated. The identification of caulerpin in other Mediterranean native fish suggests a need for further research in order to assess the possible transfer of such molecules to humans through seafood consumption

    Differential pathogenetic mechanisms of mutations in helix 2 and helix 6 of rhodopsin

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    : Variants in rhodopsin (RHO) have been linked to autosomal dominant congenital stationary night blindness (adCSNB), which affects the ability to see in dim light, and the pathogenetic mechanism is still not well understood. In this study we report two novel RHO variants found in adCSNB families, p.W265R and p.A269V, that map in the sixth transmembrane domain of RHO protein. We applied in silico molecular simulation and in vitro biochemical and molecular studies to characterize the two new variants and compare the molecular determinants to two previously characterized adCSNB variants, p.G90D and p.T94I, that map in the second transmembrane domain of the RHO protein. We demonstrate that W265R and A269V cause constitutive activation of RHO with light-independent G protein coupling and impaired binding to arrestin. Differently, G90D and T94I are characterized by slow kinetics of RHO activation and deactivation. This study provides new evidence on the differential contribution of transmembrane α-helixes two and six to the interaction with intracellular transducers of RHO and mutations in these helixes result in a similar phenotype in patients but with distinct molecular effects

    The use of Versius CMR for pelvic surgery: a multicentric analysis of surgical setup and early outcomes

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    IntroductionVersius CMR is a novel robotic system characterized by an open surgical console and independent bedside units. The system has potentials of flexibility and versatility, and has been used in urological, gynecological, and general surgical procedure. The aim is to depict a comprehensive analysis of the Versius system for pelvic surgery.MethodsThis is a study involving two Institutions, ASST Santi Paolo and Carlo, Milan, and Apuane Hospital, Massa, Italy. All interventions performed in the pelvic area with the Versius were included. Data about indications, intra-, and post-operative course were prospectively collected and analyzed.ResultsA total of 171 interventions were performed with the Versius. Forty-two of them involved pelvic procedures. Twenty-two had an oncological indication (localized prostate cancer), the remaining had a non-oncological or functional purpose. The mostly performed pelvic procedure was radical prostatectomy (22) followed by annexectomy (9). No intra-operative complication nor conversion to other approaches occurred. A Clavien II complication and one Clavien IIIb were reported. Malfunctioning/alarms requiring a power cycle of the system occurred in 2 different cases. An adjustment in trocar placement according to patients' height was required in 2 patients undergoing prostatectomy, in which the trocar was moved caudally. In two cases, a pelvic prolapse was repaired concomitant with other gynecological procedures.ConclusionsPelvic surgery with the Versius is feasible without major complications; either dissection and reconstructive steps could be accomplished, provided a proper OR setup and trocar placement are pursued. Versius can be easily adopted by surgeons of different disciplines and backgrounds; a further multi-specialty implementation is presumed and long-term oncological and functional outcomes are awaited

    On the Mathematical Constitution and Explanation of Physical Facts

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    The mathematical nature of modern physics suggests that mathematics is bound to play some role in explaining physical reality. Yet, there is an ongoing controversy about the prospects of mathematical explanations of physical facts and their nature. A common view has it that mathematics provides a rich and indispensable language for representing physical reality but that, ontologically, physical facts are not mathematical and, accordingly, mathematical facts cannot really explain physical facts. In what follows, I challenge this common view. I argue that, in addition to its representational role, in modern physics mathematics is constitutive of the physical. Granted the mathematical constitution of the physical, I propose an account of explanation in which mathematical frameworks, structures, and facts explain physical facts. In this account, mathematical explanations of physical facts are either species of physical explanations of physical facts in which the mathematical constitution of some physical facts in the explanans are highlighted, or simply explanations in which the mathematical constitution of physical facts are highlighted. In highlighting the mathematical constitution of physical facts, mathematical explanations of physical facts deepen and increase the scope of the understanding of the explained physical facts. I argue that, unlike other accounts of mathematical explanations of physical facts, the proposed account is not subject to the objection that mathematics only represents the physical facts that actually do the explanation. I conclude by briefly considering the implications that the mathematical constitution of the physical has for the question of the unreasonable effectiveness of the use of mathematics in physics

    psnGPCRdb: The Structure-network Database of G Protein Coupled Receptors

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    G protein coupled receptors (GPCRs) are critical eukaryotic signal transduction gatekeepers and represent the largest protein superfamily in the human proteome, with more than 800 members. They share seven transmembrane helices organized in an up-down bundle architecture. GPCR-mediated signaling pathways have been linked to numerous human diseases, and GPCRs are the targets of approximately 35% of all drugs currently on the market. Structure network analysis, a graph theory-based approach, represents a cutting-edge tool to deeply understand GPCR function, which strongly relies on communication between the extracellular and intracellular poles of their structure. psnGPCRdb stores the structure networks (i.e., linked nodes, hubs, communities and communication pathways) computed on all updated GPCR structures in the Protein Data Bank, in their isolated states or in complex with extracellular and/or intracellular molecules. The structure communication signatures of a sub-family or family of GPCRs as well as of their small-molecule activators or inhibitors are stored as consensus networks. The database stores also all meaningful structure network-based comparisons (i.e., difference networks) of functionally different states (i.e., inactive or active) of a given receptor sub-type, or of consensus networks representative of a receptor sub-type, type, sub-family or family. Single or consensus GPCR networks hold also information on amino acid conservation. The database allows to graphically analyze 3D structure networks together with interactive data-tables. Ligand-centric networks can be analyzed as well. psnGPCRdb is unique and represents a powerful resource to unravel GPCR function with important implications in cell signaling and drug design. psnGPCRdb is freely available at: http://webpsn.hpc.unimo.it/psngpcr.php

    Short-term physiological and biometrical responses of Lepidium sativum seedlings exposed to PET-made microplastics and acid rain

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    Plastics enter in terrestrial natural system primarily by agricultural purposes, while acid rain is the result of anthropogenic activities. The synergistic effects of microplastics and acid rain on plant growth are not known. In this study, different sizes of polyethylene terephthalate (PET) and acid rain are tested on Lepidium sativum, in two separate experimental sets. In the first one we treated plants only with PET, in the second one we used PET and acid rain together. In both experimentations we analyzed: i) plant biometrical parameters (shoot height, leaf number, percentage inhibition of seed germination, fresh biomass), and ii) oxidative stress responses (hydrogen peroxide; ascorbic acid and glutathione). Results carried out from our experiments highlighted that different sizes of polyethylene terephthalate are able to affect plant growth and physiological responses, with or without acid rain supplied during acute toxicity (6 days). Short description: This study showed that different sizes of PET microplastics affect physiological and biometrical responses of Lepidum sativum seedlings, with or without acid rain; roots and leaves responded differently
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